Virtual machine (VM) software currently enables users to run multiple operating systems on a single physical machine by supporting VM bundles that encapsulate an entire hard disk as well as the state of the system RAM (random-access memory). Users often need to run the multiple VMs based on the same operating system. For example, one may want to run two Microsoft XP operating system images and two Linux operating system images in the same computer. It is wasteful to replicate the same OS system files in all of the XP images or in all of the Linux images. Consider, for example, an upgrade patch to be downloaded for upgrading an application program or the operating system. When multiple images exist, all must be modified to keep them in synchronization. Therefore, there is a need for a method and system that overcomes the above wasteful replication.